I’ve been looking at doing an analysis with some protein subfamily sequence logos, using Eric Beitz’s texshade. While it’s a little strange that it does the actual analysis part (rather than just the rendering) using LaTeX, it’s the only implementation of the method I know of, and it beats reimplementing it from the paper.
Although it was published in 2006 (and earlier in 2000), with the original URLs now dead, I noticed the latest update for the version of texshade in CTAN (v1.18) was on 15th of April, 2008 … ie texshade was updated just 14 days ago !
It happens all to often that published bioinformatics tools cease to be updated or even disappear from the Web not long after the peer-review publication is released. Kudos to Eric for not abandoning his software.